Thesis

Comparative Analysis of DNA Methylation between Calcifying and non-Calcifying Strains of Emiliania Huxleyi

Methylation of cytosine in DNA is an epigenetic change associated with gene regulation. This paper presents a study of the effects of epigenetic modifications associated with DNA methylation on expression and regulation of bio-mineralization genes in two strains of marine algae Emiliania huxleyi (E. huxleyi); the calcifying (PLY 217) and non-calcifying (CCMP-1516) strains.
 Using Bismark bisulfite sequence analysis tools, we mapped genome methylation across the genomes of a calcifying (PLY 217) and non-calcifying (CCMP-1516) strains Emiliania huxleyi (E. huxleyi); and generated methylation profiles for both strains, PLY 217 and CCMP-1516. Using methylKit and genomation R packages, we correlated differential methylation with gene expression profiles. 
 A comparison analysis was performed using MOABS to validate Bismark results. The analyses were extended using custom R codes to identify differentially methylated regions and related gene annotation from upstream and downstream gene regions along with graphical R plots and Venn diagrams to illustrate the results. 
 At the end, a list of unique genes, located in differentially methylated regions, detected using both Bismark and Moabs alignment tools. The list presented in a dataset containing complete gene annotations.

Methylation of cytosine in DNA is an epigenetic change associated with gene regulation. This paper presents a study of the effects of epigenetic modifications associated with DNA methylation on expression and regulation of bio-mineralization genes in two strains of marine algae Emiliania huxleyi (E. huxleyi); the calcifying (PLY 217) and non-calcifying (CCMP-1516) strains. Using Bismark bisulfite sequence analysis tools, we mapped genome methylation across the genomes of a calcifying (PLY 217) and non-calcifying (CCMP-1516) strains Emiliania huxleyi (E. huxleyi); and generated methylation profiles for both strains, PLY 217 and CCMP-1516. Using methylKit and genomation R packages, we correlated differential methylation with gene expression profiles. A comparison analysis was performed using MOABS to validate Bismark results. The analyses were extended using custom R codes to identify differentially methylated regions and related gene annotation from upstream and downstream gene regions along with graphical R plots and Venn diagrams to illustrate the results. At the end, a list of unique genes, located in differentially methylated regions, detected using both Bismark and Moabs alignment tools. The list presented in a dataset containing complete gene annotations.

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